Have you checked the sizing of the condensate header, considering the effect of flash steam?  As your liquid condensate is throttled by the trap from a high pressure (on the HX) to a lower pressure (in the condensate return), a fraction of the liquid will flash to vapor in an isenthalpic process.

A rule of thumb is to have the vapor velocity in the condensate header < 50 ft/s.  If it is too fast, the liquid in the bottom of the line can be picked up in waves and convert to plug flow.  This will cause waterhammer at elbows, valves, or reducers.  Even with a very small mass percentage of the condensate flashing to vapor, the vapor will occupy nearly all of the volume.  Also, it is best to minimize vertical rises in the condensate line.

I couldn't answer it better than that.  A great reference for problems with steam systems is the Spirax/Sarco "Design of Fluid Systems".  This book can be obtained from your local rep.

Another item that you may consider is vertical drop from the heater.  If there is no vertical condensate collector, you could get blow through when the trap opens.

Do you have temperature controller in this system? If your answer is yes, please install a vacuum breaker in condensate line before the trap or in the HX.

You need to check the type of check valves that are being used in the system. Water hammer also results when the wrong check valves are installed such as, swing checks & double door designs, they close after the reverse flow pressure slams them to the seat. This is most evident when using swing check design which is 9 times out of 10. Swing checks are also the worst choice for steam & condensate because of the poor shut off capability. Even when they are new the shut off is less than ANSI class IV. They leak way too much from day one. Thus your reverse flow can be significant when new, and gets worse as the valve ages. As the system ages so does the swing checks and as a result the reverse flow continues worsen causing the water hammer to get louder and louder. When reverse flow causes severe water hammer the flapper will sometimes fail breaking into pieces which may cause progressive damage to other equipment as they flow downstream. Some people will go to the extreme of replacing the entire trap system when all they needed to do is put the correct check valves in. The most reputable trap manufacturers use Durabla Fluid Technology which makes the most reliable in-line silent check valve in the market for your application. Original equipment manufacturers (OEM's)such as Armstrong & Spirax Sarco & others use Durabla on all the traps they sell where water hammer conditions cause these types of problems. This design eliminates the water hammer and when the valve ages and the spring fails beyond its million cycle design the valve will continue to provide superior shutoff. When this occurs you simply replace the old spring with a new one and your back in business.